documentation

screenshots

Figure 1. A view of a running pipeline in Ergatis. Click to view other screenshots.

description

Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis
pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components
can be arranged graphically to form highly-configurable pipelines. Each analysis component supports
multiple output formats, including the Bioinformatic Sequence Markup
Language (BSML). The current implementation includes support for data loading into project databases
following the CHADO schema, a highly normalized,
community-supported schema for storage of biological annotation data.

Ergatis uses the Workflow engine to process
its work on a compute grid. Workflow provides an XML
language and processing engine for specifying the steps of a computational pipeline. It provides detailed
execution status and logging for process auditing, facilitates error recovery from point of failure, and
is highly scalable with support for distributed computing environments. The XML format employed enables
commands to be run serially, in parallel, and in any combination or nesting level.

This framework has been employed in the annotation of several large, eukaryotic organisms, including
Aedes aegypti and Trichomonas vaginalis.